Bio::DB::GFF::Aggregator::alignment -- Alignment aggregator
use Bio::DB::GFF; # Open the sequence database my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql', -dsn => 'dbi:mysql:elegans42', -aggregator => ['alignment'], ); ----------------------------- Aggregator method: alignment Main method: (none) Sub methods: nucleotide_match,EST_match,cDNA_match,expressed_sequence_match, translated_nucleotide_match,protein_match,HSP -----------------------------
Bio::DB::GFF::Aggregator::alignment is one of the default aggregators, and was written to be compatible with the C elegans GFF files. It aggregates raw "similarity" features into composite features of type "alignment". A better name for this class might be "gapped_alignment."
This aggregator does not insist that there be a single top-level feature that spans one end of the alignment to the other. As a result, it can produce truncated alignments if the entire alignment is not contained within the segment of interest.
Title : aggregate Usage : $features = $a->aggregate($features,$factory) Function: aggregate a feature list into composite features Returns : an array reference containing modified features Args : see L<Bio::DB::GFF::Aggregator> Status : Public
Because of the large number of similarity features, the aggregate() method is overridden in order to perform some optimizations.
Title : method Usage : $aggregator->method Function: return the method for the composite object Returns : the string "alignment" Args : none Status : Public
Title : part_names Usage : $aggregator->part_names Function: return the methods for the sub-parts Returns : the full list of aggregated methods Args : none Status : Public